Peptide Molecular Weight Calculator

Calculate molecular weight, isoelectric point (pI), net charge, extinction coefficient, and amino acid composition from peptide sequences.

Enter peptide sequence (1-letter or 3-letter codes)

<button class="btn" onclick="calculate()">Calculate</button>
<button class="btn btn-ghost" onclick="document.getElementById('seq').value='';document.getElementById('results').className='results'">Clear</button>
</div>
<div style="margin-top:12px">
<span style="color:#64748b;font-size:0.75em">Try an example:</span>
<button class="example-btn" onclick="document.getElementById('seq').value='GCKRLVQGLP';calculate()">GCKRLVQGLP</button>
<button class="example-btn" onclick="document.getElementById('seq').value='A R N D C E Q G H I L K M F P S T W Y V';calculate()">All 20 AAs</button>
<button class="example-btn" onclick="document.getElementById('seq').value='H-Aib-EGTFTSDVSSYLEGQAAKEFIAWLVKGR-NH2';calculate()">Semaglutide</button>
<button class="example-btn" onclick="document.getElementById('seq').value='H-YAEGTFISDYSIAMDKIHQQDFVNWLLAQKGKKNDWKHNITQ-NH2';calculate()">Tirzepatide</button>
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<div class="notes">
<strong>How it works:</strong> Calculates monoisotopic molecular weight using standard amino acid residue masses (internal residues lose H₂O, N-terminal adds H, C-terminal adds OH). Isoelectric point (pI) calculated via iterative pH search using Henderson-Hasselbalch equation. Net charge at pH 7. Extinction coefficient at 280nm based on Trp, Tyr, and cystine content.
</div>

<div class="internal-links">
<h3>Related Resources</h3>
<a href="/blog/peptide-storage-guide">Peptide Storage & Handling Guide — Proper storage temperatures and reconstitution</a>
<a href="/blog/coa-purity-guide">How to Read a Certificate of Analysis (COA) — Understanding HPLC and mass spec</a>
<a href="/blog/research-peptides-guide">Research Peptides: A Comprehensive Guide — Sourcing, handling, and analysis</a>
<a href="/shop">Browse Our Catalog — 137+ research peptides and chemicals</a>
</div>
</div>

function seqToOneLetter(seq){
let parsed=parseSequence(seq);
return parsed.map(a=>a.l).join('');
}

function calculate(){
let seq=document.getElementById('seq').value.trim();
if(!seq){alert('Please enter a peptide sequence');return}
let parsed=parseSequence(seq);
if(parsed.length===0){alert('Could not parse sequence. Use 1-letter codes (ARNDC...) or 3-letter codes (Ala-Arg-Asn-...)');return}
let oneLetter=parsed.map(a=>a.l).join('');

// Molecular weight (monoisotopic)
let mw=18.01528; // H + OH (termini)
for(let aa of parsed)mw+=aa.mw;

// Net charge at pH 7
let pH=7.0;
let nTermPka=parsed[0].pkn;
let cTermPka=parsed[parsed.length-1].pkc;
let charge=0;
// N-terminus
charge+=1/(1+Math.pow(10,pH-nTermPka));
// C-terminus  
charge-=1/(1+Math.pow(10,cTermPka-pH));
// Side chains
for(let aa of parsed){
if(aa.pkr>0){
if(aa.l==='R'||aa.l==='K'||aa.l==='H')charge+=1/(1+Math.pow(10,pH-aa.pkr));
else if(aa.l==='D'||aa.l==='E'||aa.l==='C'||aa.l==='Y')charge-=1/(1+Math.pow(10,aa.pkr-pH));
}
}

// Isoelectric point
let pI=7.0;
let minCharge=999;
for(let testPh=0.5;testPh<=14;testPh+=0.05){
let c=0;
c+=1/(1+Math.pow(10,testPh-nTermPka));
c-=1/(1+Math.pow(10,cTermPka-testPh));
for(let aa of parsed){
if(aa.pkr>0){
if(aa.l==='R'||aa.l==='K'||aa.l==='H')c+=1/(1+Math.pow(10,testPh-aa.pkr));
else if(aa.l==='D'||aa.l==='E'||aa.l==='C'||aa.l==='Y')c-=1/(1+Math.pow(10,aa.pkr-testPh));
}
}
let absC=Math.abs(c);
if(absC<minCharge){minCharge=absC;pI=testPh}
}

// Extinction coefficient (280nm)
let nW=0,nY=0,nC=0;
for(let aa of parsed){
if(aa.l==='W')nW++;
if(aa.l==='Y')nY++;
if(aa.l==='C')nC++;
}
let extCoeff=nW*5500+nY*1490+Math.floor(nC/2)*125; // M⁻¹cm⁻¹

// Composition
let comp={};
for(let aa of parsed){
comp[aa.l]=comp[aa.l]?comp[aa.l]+1:1;
}
let maxComp=Math.max(...Object.values(comp));

// Render
let html='';
html+='<div class="result-grid">';
html+=`<div class="result-card"><div class="result-value">${mw.toFixed(2)} Da</div><div class="result-label">Monoisotopic Molecular Weight</div></div>`;
html+=`<div class="result-card"><div class="result-value">${pI.toFixed(2)}</div><div class="result-label">Isoelectric Point (pI)</div></div>`;
html+=`<div class="result-card"><div class="result-value">${charge>=0?'+'+charge.toFixed(2):charge.toFixed(2)}</div><div class="result-label">Net Charge at pH 7</div></div>`;
html+=`<div class="result-card"><div class="result-value">${extCoeff}</div><div class="result-label">Extinction Coefficient (M⁻¹cm⁻¹ at 280nm)</div></div>`;
html+=`<div class="result-card"><div class="result-value">${parsed.length}</div><div class="result-label">Residues</div></div>`;
html+=`<div class="result-card"><div class="result-value">${oneLetter}</div><div class="result-label">Sequence (1-letter)</div></div>`;
html+='</div>';

// Composition chart
html+='<div class="result-card"><div class="result-label">Amino Acid Composition</div>';
html+='<div class="bar-chart">';
for(let aa of 'ACDEFGHIKLMNPQRSTVWY'){
let count=comp[aa]||0;
let h=count/maxComp*100;
html+=`<div class="bar-col"><div class="bar-fill" style="height:${h}px" title="${AA[aa].t}: ${count}"></div><div class="bar-label">${aa}</div></div>`;
}
html+='</div></div>';

// Composition table
html+='<table class="comp-table"><thead><tr><th>AA</th><th>Name</th><th>Count</th><th>%</th><th>Residue MW</th></tr></thead><tbody>';
for(let aa of 'ACDEFGHIKLMNPQRSTVWY'){
let count=comp[aa]||0;
if(count>0){
html+=`<tr><td>${aa}</td><td>${AA[aa].t}</td><td>${count}</td><td>${(count/parsed.length*100).toFixed(1)}%</td><td>${AA[aa].mw.toFixed(2)}</td></tr>`;
}
}
html+='</tbody></table>';

document.getElementById('results').innerHTML=html;
document.getElementById('results').className='results active';
}
</script>
<script type="application/ld+json">
{
"@context":"https://schema.org",
"@type":"SoftwareApplication",
"name":"Peptide Molecular Weight Calculator",
"applicationCategory":"ScienceApplication",
"operatingSystem":"Web Browser",
"description":"Calculate molecular weight, isoelectric point, net charge, and amino acid composition from peptide sequences.",
"url":"https://polypeptides.store/tools/peptide-calculator",
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</body>
</html>